Evolutionary Analysis

Tree

Mathematical structure

Model evolutionary history

Taxon 1

Taxon 2

Taxon 3

Taxon 4

Taxon 5

Taxon 6

Taxon 1

Taxon 2

Taxon 3

Taxon 4

Taxon 5

Taxon 6

Sister taxa

Outgroup

Root

Branch

Node

Tip

Polytomy (more than one branch emerging from one node)

(a) The astragalus is a synapomorphy that identifiesartiodactyls as a monophyletic group.

Camel

Peccary

Pig

Hippo

Whale

Deer

Cow

Astragalus(ankle bone)

ARTIODACTYLS

Gain of pulley-shaped astragalus

(b) If whales are related to hippos, then two changesoccurred in the astragalus.

Camel

Peccary

Pig

Hippo

Whale

Deer

Cow

ARTIODACTYLS

Gain of pulley-shaped astragalus

Loss of pulley-shaped astragalus

(a) The astragalus is a synapomorphy that identifiesartiodactyls as a monophyletic group.

(b) If whales are related to hippos, then two changesoccurred in the astragalus.

Camel

Peccary

Pig

Hippo

Whale

Deer

Cow

Camel

Peccary

Pig

Hippo

Whale

Deer

Cow

(c) Data on the presence and absence of SINE genes support the close relationship between whales and hippos.

Cow

Locus

DeerWhaleHippoPigPeccaryCamel

Astragalus(ankle bone)

1 gene present0 gene absent? still undetermined

Whales and hippos share fourunique SINE genes (4, 5, 6, and 7)

ARTIODACTYLS

ARTIODACTYLS

Gain of pulley-shaped astragalus

Loss of pulley-shaped astragalus

Gain of pulley-shaped astragalus

Phylogenetic Tree

shows ancestor-descendent relationships among populations or species

clarifies evolutionary relationships

Root

Ancestor of all sequences on tree

Taxon 1

Taxon 2

Taxon 3

Taxon 4

Taxon 5

Taxon 6

Sister taxa

Outgroup

Root

Branch

Node

Tip

Polytomy (more than one branch emerging from one node)

Taxon 1

Taxon 2

Taxon 3

Taxon 4

Taxon 5

Taxon 6

Taxon 1

Taxon 3

Taxon 2

Taxon 4

Taxon 5

Taxon 6

(a) (b) (c)1

2

3

4

5

6

1

6

5

4

3

2

2

4

5

6

3

1

(a) (b) (c)1

2

3

4

5

6

1

6

5

4

3

2

2

4

5

6

3

1

= =

Types of Trees

Rooted

Unrooted

Rooted Trees

Node identified as root, from which all other nodes descend

Have direction corresponding to evolutionary time

Taxon 1

Taxon 2

Taxon 3

Taxon 4

Taxon 5

Taxon 6

Sister taxa

Outgroup

Root

Branch

Node

Tip

Polytomy (more than one branch emerging from one node)

Unrooted Trees

Lacks root

Does not specify evolutionary relationships

Nothing about ancestors and descendents

Unrooted Trees

Lacks root

Does not specify evolutionary relationships

Nothing about ancestors and descendents

Many tree-building programs generate unrooted trees!

Types of Trees

Cladogram

Phylogram

Cladogram

Cladogram

Relative recency of common ancestry

Cladogram

Cladogram

Relative recency of common ancestry

Does not show amount of evolutionary change

Phylogram

Phylogram

Also contains branch lengths

Numbers associated with branches

Amount of evolutionary change

Phylogram

Cladogram

Phylogram

Constructing a Tree

Construct multiple sequence alignment

Build Tree

Evaluate Tree

So how do I build a tree?

So how do I build a tree?

http://www.phylogeny.fr/

http://expasy.org/tools/

http://evolution.genetics.washington.edu/phylip/software.html#methods

So how do I build a tree?http://www.phylogeny.fr/

Tree building programs

Tree drawing programs

FASTA alignment

Newick Format

(((((((Prochlorococcus_marinus:0.499642,Synechococcus_BL107:0.212828)0.961000:0.131562,Cyanobium_PCC7001:0.279338)0.984000:0.159534,Thiomicrospira_crunogena:0.805902)0.230000:0.067881,Allochromatium_vinosum:0.522452)0.974000:0.136543,(Bradyrhizobium_BTAi1:1.004711,Nitrobacter_hamburgensis:0.728510)0.596000:0.070606)0.895000:0.088934,Halothiobacillus_neapolitanus:0.624513)0.987000:0.172336,Acidimicrobium_ferrooxidans:0.338388,Acidithiobacillus_ferrooxidans:0.255268);

Tree drawing programs

File formats to save your tree

http://www.phylogeny.fr/

Evaluating Trees

Do your results make sense?

Evaluating Trees

Do your results make sense?

resample your data

Bootstrap treebranch support values

Evaluating Trees

Do your results make sense?

resample your data

ground-truth your data

www.ncbi.nlm.nih.gov

http://rdp.cme.msu.edu/

www.ncbi.nlm.nih.gov

Organism Trees vs Gene Trees

Don’t always match!

Homologs

Orthologs

separated by speciation

Paralogs

produced by gene duplication

Xenologs

result of horizontal gene transfer

Tree-building resources

http://www.phylogeny.fr/

http://expasy.org/tools/

http://evolution.genetics.washington.edu/phylip/software.html#methods